CVR - Coronavirus Vaccines R&D Roadmap

Milestone
1.1.b

Sequencing capacity

In progress

Enhance global capacity to generate and share genomic data from SARS-CoV-2 and other human coronaviruses, particularly in low-resource settings, to inform global surveillance efforts.

Progress Highlights

Vijayasimha & Srikanth 2026 propose the following internationally benchmarked operational standards to strengthen early-warning systems for HKU5-CoV-2 spillover prevention: 1) a “time-to-signal” metric requiring detection of a novel zoonotic coronavirus within ≤7 days from sentinel sampling to public data deposition, 2) predefined surge-sequencing triggers, such as ≥3 epidemiologically linked atypical pneumonia clusters at an animal–human interface within 14 days, and 3) minimum genomic surveillance coverage targets of ≥5% sequencing of severe respiratory cases in high-risk regions during peacetime, scalable to ≥20% during alert phases.

Khoo 2025 proposed a set of considerations for establishing pathogen genomic surveillance systems in low-resource settings, although quantifying the exact costs versus benefits of genomic surveillance is a challenge.

Wohl 2023 developed sample size calculations for variant detection and variant prevalence from whole-genome sequences based on the surveillance model; to determine whether low-resource countries are meeting the sample size requirement, sequence data from the Global Initiative for Sharing All Influenza Data (GISAID) EpiCoV database can be utilized.

Some tools developed earlier in the pandemic to monitor GISAID submissions automatically by country (CoVariants) or country income classification (FIND) are no longer being updated regularly; others that are updated regularly, such as Nextstrain Forecasts, are biased towards high income countries that meet sequence volume requirements. As of October 2025, GISAID is no longer sharing data with Nextstrain, further complicating efforts to monitor SARS-CoV-2 evolution.

Several studies from low or lower middle income countries have been published over the past few years indicating that sequencing capacity exists, but the data are so retrospective that the variants described are no longer in circulation at the time of publication, and therefore cannot inform timely global surveillance efforts.